LongHap is writen for individual genome phasing based on the alignment and variantion results generated from stLFR and NGS 
technology. Latest version was v1.3 upload in 10/17/2018.

Usage:
  perl Main.pl <indexed sorted bam> <vcf> <window size> <max LFR> <min SupportBarcodes> <min Link> <shellDir> <outDir_tmp> 
  <outDir_final>

Detailed Description:
  <indexed sorted bam> is an alignment file in BAM format which must be sorted and indexed in advance
  <vcf> shoud store variant calling result in VCF format
  <window size> is set for each phasing window, 10MB is suggested
  <max LFR> is decided by the maximum length of DNA fragment. Normally it is not larger than 300KB according to the current 
  stretage of stLFR technology.
  <min SupportBarcodes> is the minimum count of supporting barcode for each variant
  <min Link> is the minimum count of linked info
  <shellDir> is an directory storing shell scripts which need to be executed, absolute path is suggested
  <outDir_tmp> is a temporary directory storing split phasing result as well as barcode supporting info, absolute path is 
  suggested
  <outDir_final> is a directory storing the final phasing result in chr*.vcf files, absolute path is suggested.

Example:
  perl Main.pl input.bam input.vcf 10000000 300000 1 1 shellDir outDir_tmp outDir_final  
  After running this command, you will find 23 shell scripts in shellDir, with the names of "run.chr1.sh" or "run.chrX.sh", 
which could be executed parallelly. In average, each chromosome costs 2~3 hours by consuming 4GB memory.The final phasing 
results can be found in outDir_final dir in chr*.vcf files, while the medium files storing barcode supporting info can be 
found in the outDir_tmp dir.

Author: 
  Yuhui Sun

Email:
  sunyuhui@genomics.cn
